doc: private / public / fix references

[dweindl]

• Exclude private members from the sphinx documentation
• Make some supposed-to-be-private members private
• Fix references

To be continued...

[codecov]

Codecov Report

❌ Patch coverage is 84.46602% with 32 lines in your changes missing coverage. Please review.
✅ Project coverage is 77.60%. Comparing base (6b3bf83) to head (d7f9c1e).
⚠️ Report is 1 commits behind head on main.

Files with missing lines	Patch %	Lines
python/sdist/amici/importers/sbml/__init__.py	83.75%	32 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #3096      +/-   ##
==========================================
- Coverage   78.18%   77.60%   -0.59%     
==========================================
  Files         315      315              
  Lines       20481    20466      -15     
  Branches     1500     1500              
==========================================
- Hits        16014    15882     -132     
- Misses       4458     4575     +117     
  Partials        9        9              

Flag	Coverage Δ
cpp	71.73% <83.00%> (+0.06%)	⬆️
cpp_python	37.73% <63.10%> (+0.05%)	⬆️
petab	46.46% <74.75%> (+0.06%)	⬆️
petab_sciml	13.79% <54.36%> (+0.04%)	⬆️
python	70.37% <84.46%> (+0.06%)	⬆️
sbmlsuite-jax	?

Flags with carried forward coverage won't be shown. Click here to find out more.

Files with missing lines	Coverage Δ
python/sdist/amici/__init__.py	95.16% <ø> (ø)
python/sdist/amici/adapters/fiddy.py	89.56% <100.00%> (+11.04%)	⬆️
python/sdist/amici/exporters/sundials/de_export.py	96.38% <ø> (ø)
python/sdist/amici/importers/antimony/__init__.py	83.33% <ø> (ø)
...thon/sdist/amici/importers/petab/v1/sbml_import.py	97.75% <ø> (ø)
python/sdist/amici/importers/pysb/__init__.py	94.64% <ø> (ø)
python/sdist/amici/importers/sbml/splines.py	80.62% <100.00%> (ø)
python/sdist/amici/importers/utils.py	83.33% <ø> (-2.71%)	⬇️
python/tests/conftest.py	43.33% <ø> (ø)
python/tests/test_petab_import.py	100.00% <ø> (ø)
... and 1 more

... and 3 files with indirect coverage changes

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